Merge pull request #767 from AFM-SPM/ns-rse/scientific-python-pre-commit

No substantial change to code all linting changes so merging without approval. + [codespell](https://github.com/codespell-project/codespell) checks spelling in code files. + [prettier](https://github.com/prettier/prettier) lints files other than Python.
AFM-SPM · Dec 19, 2023 · 67e298b · 67e298b
2 parents 3f94eb5 + 3adbc6c
commit 67e298b
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diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -1,3 +1,6 @@
+# codespell
+e9f1c8fa0904d643285901110e7a026f3427dc15
+
 # ruff - isort and numpy linting
 9e0502b9cce2257d6234f118091cb75dd07c21ee
 8d1729e7a4132e88562a8f6b1514a95abd8878c1

diff --git a/.github/ISSUE_TEMPLATE/bug_report.yaml b/.github/ISSUE_TEMPLATE/bug_report.yaml
@@ -1,9 +1,9 @@
 name: Bug report
 description: Create a report to help us improve
-title: '[Bug]: '
-labels: 'bug'
+title: "[Bug]: "
+labels: "bug"
 assignees:
-  - ''
+  - ""
 body:
   - type: markdown
     attributes:

diff --git a/.github/ISSUE_TEMPLATE/feature_request.yaml b/.github/ISSUE_TEMPLATE/feature_request.yaml
@@ -1,9 +1,9 @@
 name: Feature request
 description: Suggest an idea for this project
-title: '[feature] : '
-labels: 'enhancement'
+title: "[feature] : "
+labels: "enhancement"
 assignees:
-  - ''
+  - ""
 body:
   - type: markdown
     attributes:

diff --git a/.github/workflows/ORDA.yaml b/.github/workflows/ORDA.yaml
@@ -10,7 +10,7 @@ jobs:
       ARCHIVE_NAME: ${{ github.event.repository.name }}-${{ github.event.release.tag_name }}
     steps:
       - name: prepare-data-folder
-        run : mkdir 'data'
+        run: mkdir 'data'
       - name: download-archive
         run: |
           curl -sL "${{ github.event.release.zipball_url }}" > "$ARCHIVE_NAME".zip
@@ -23,6 +23,6 @@ jobs:
         uses: figshare/github-upload-action@v1
         with:
           FIGSHARE_TOKEN: ${{ secrets.FIGSHARE_TOKEN }}
-          FIGSHARE_ENDPOINT: 'https://api.figshare.com/v2'
+          FIGSHARE_ENDPOINT: "https://api.figshare.com/v2"
           FIGSHARE_ARTICLE_ID: 22633528
-          DATA_DIR: 'data'
+          DATA_DIR: "data"
diff --git a/.github/workflows/pypi.yaml b/.github/workflows/pypi.yaml
@@ -4,7 +4,7 @@ on:
   push:
     tags:
       - v*
-  workflow_dispatch:        # Uncomment line if you also want to trigger action manually
+  workflow_dispatch: # Uncomment line if you also want to trigger action manually
 
 jobs:
   build-release:

diff --git a/.github/workflows/sphinx_docs_to_gh_pages.yaml b/.github/workflows/sphinx_docs_to_gh_pages.yaml
@@ -6,7 +6,7 @@ on:
     # Uncomment if only tagged releases are to have documentation built
     # tags:
     #   - v*
-  workflow_dispatch:        # Uncomment line if you also want to trigger action manually
+  workflow_dispatch: # Uncomment line if you also want to trigger action manually
 
 jobs:
   sphinx_docs_to_gh-pages:
@@ -32,8 +32,8 @@ jobs:
           # defined as it defaults to 'main'.
           branch: main
           dir_docs: docs
-          sphinxapiexclude: '../*setup* ../*tests* ../*.ipynb ../demo.py ../make_baseline.py ../jupyter_notebook_config.py ../demo_ftrs.py'
-          sphinxapiopts: '--separate -o . ../'
-          sphinxopts: ''
+          sphinxapiexclude: "../*setup* ../*tests* ../*.ipynb ../demo.py ../make_baseline.py ../jupyter_notebook_config.py ../demo_ftrs.py"
+          sphinxapiopts: "--separate -o . ../"
+          sphinxopts: ""
           multiversion: true
-          multiversionopts: ''
+          multiversionopts: ""
diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml
@@ -16,7 +16,7 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
-        python-version: ['3.9', '3.10', '3.11']
+        python-version: ["3.9", "3.10", "3.11"]
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0  # Use the ref you want to point at
+    rev: v4.5.0 # Use the ref you want to point at
     hooks:
       - id: check-case-conflict
       - id: check-docstring-first
@@ -33,17 +33,34 @@ repos:
     rev: v0.1.8
     hooks:
       - id: ruff
-        args: [ --fix, --exit-non-zero-on-fix, --show-fixes ]
+        args: [--fix, --exit-non-zero-on-fix, --show-fixes]
 
   - repo: https://github.com/psf/black-pre-commit-mirror
     rev: 23.12.0
     hooks:
       - id: black
         types: [python]
-        additional_dependencies: ['click==8.0.4']
+        additional_dependencies: ["click==8.0.4"]
         args: ["--extend-exclude", "topostats/plotting.py"]
       - id: black-jupyter
 
+  - repo: https://github.com/adamchainz/blacken-docs
+    rev: 1.16.0
+    hooks:
+      - id: blacken-docs
+        additional_dependencies:
+          - black==22.12.0
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.6
+    hooks:
+      - id: codespell
+
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v3.1.0
+    hooks:
+      - id: prettier
+
   - repo: https://github.com/kynan/nbstripout
     rev: 0.6.1
     hooks:
@@ -60,7 +77,7 @@ repos:
 
 ci:
   autofix_prs: true
-  autofix_commit_msg: '[pre-commit.ci] Fixing issues with pre-commit'
+  autofix_commit_msg: "[pre-commit.ci] Fixing issues with pre-commit"
   autoupdate_schedule: weekly
-  autoupdate_commit_msg: '[pre-commit.ci] pre-commit-autoupdate'
+  autoupdate_commit_msg: "[pre-commit.ci] pre-commit-autoupdate"
   skip: [pylint] # Optionally list ids of hooks to skip on CI
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -5,6 +5,12 @@
 # Required
 version: 2
 
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/conf.py
@@ -19,7 +25,7 @@ formats:
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: '3.8'
+  version: "3.8"
   install:
     - method: pip
       path: .

diff --git a/CITATION.cff b/CITATION.cff
@@ -12,32 +12,32 @@ authors:
     family-names: Pyne
     email: a.l.pyne@sheffield.ac.uk
     affiliation: The University of Sheffield
-    orcid: 'https://orcid.org/0000-0002-2658-8987'
+    orcid: "https://orcid.org/0000-0002-2658-8987"
   - given-names: Robert
     family-names: Turner
     email: r.d.turner@sheffield.ac.uk
     affiliation: The University of Sheffield
-    orcid: 'https://orcid.org/0000-0002-1353-1404'
+    orcid: "https://orcid.org/0000-0002-1353-1404"
   - given-names: Neil
     family-names: Shephard
     email: n.shephard@sheffield.ac.uk
     affiliation: The University of Sheffield
-    orcid: 'https://orcid.org/0000-0001-8301-6857'
+    orcid: "https://orcid.org/0000-0001-8301-6857"
   - given-names: Syliva
     family-names: Whittle
     email: sylvia.whittle@sheffield.ac.uk
     affiliation: The University of Sheffield
-    orcid: 'https://orcid.org/0009-0008-9164-9513'
+    orcid: "https://orcid.org/0009-0008-9164-9513"
   - given-names: Max
     family-names: Gamill
     email: mcgamill1@sheffield.ac.uk
     affiliation: The University of Sheffield
-    orcid: 'https://orcid.org/0009-0007-3250-5299'
+    orcid: "https://orcid.org/0009-0007-3250-5299"
   - email: mdu12@sheffield.ac.uk
     affiliation: The University of Sheffield
     given-names: Mingxue
     family-names: Du
-    orcid: 'https://orcid.org/0009-0008-9452-5719'
+    orcid: "https://orcid.org/0009-0008-9452-5719"
 identifiers:
   - type: doi
     value: 10.15131/shef.data.22633528.v1
@@ -53,4 +53,4 @@ keywords:
 license: GPL-3.0
 commit: cd0ec35a5071deb7f6f8ef6dce6598a542cb059b
 version: 2.1.0
-date-released: '2023-05-18'
+date-released: "2023-05-18"
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
@@ -17,23 +17,23 @@ diverse, inclusive, and healthy community.
 Examples of behavior that contributes to a positive environment for our
 community include:
 
-* Demonstrating empathy and kindness toward other people
-* Being respectful of differing opinions, viewpoints, and experiences
-* Giving and gracefully accepting constructive feedback
-* Accepting responsibility and apologizing to those affected by our mistakes,
+- Demonstrating empathy and kindness toward other people
+- Being respectful of differing opinions, viewpoints, and experiences
+- Giving and gracefully accepting constructive feedback
+- Accepting responsibility and apologizing to those affected by our mistakes,
   and learning from the experience
-* Focusing on what is best not just for us as individuals, but for the
+- Focusing on what is best not just for us as individuals, but for the
   overall community
 
 Examples of unacceptable behavior include:
 
-* The use of sexualized language or imagery, and sexual attention or
+- The use of sexualized language or imagery, and sexual attention or
   advances of any kind
-* Trolling, insulting or derogatory comments, and personal or political attacks
-* Public or private harassment
-* Publishing others' private information, such as a physical or email
+- Trolling, insulting or derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information, such as a physical or email
   address, without their explicit permission
-* Other conduct which could reasonably be considered inappropriate in a
+- Other conduct which could reasonably be considered inappropriate in a
   professional setting
 
 ## Enforcement Responsibilities
@@ -106,7 +106,7 @@ Violating these terms may lead to a permanent ban.
 ### 4. Permanent Ban
 
 **Community Impact**: Demonstrating a pattern of violation of community
-standards, including sustained inappropriate behavior,  harassment of an
+standards, including sustained inappropriate behavior, harassment of an
 individual, or aggression toward or disparagement of classes of individuals.
 
 **Consequence**: A permanent ban from any sort of public interaction within

diff --git a/README.md b/README.md
@@ -25,9 +25,10 @@ status](https://results.pre-commit.ci/badge/github/AFM-SPM/TopoStats/main.svg)](
 
 | [Installation](#installation) | [Tutorials and Examples](#tutorials-and-examples) | [Contributing](contributing.md) |
 [Licence](#licence) | [Citation](#citation) |
+
 </div>
 
---------------------------------------------------------------------------------
+---
 
 An AFM image analysis program to batch process data and obtain statistics from images.
 
@@ -37,7 +38,7 @@ There is more complete documentation on the projects [documentation website](htt
 
 TopoStats is available via PyPI and can be installed in your Virtual Environment with...
 
-``` bash
+```bash
 pip install topostats
 ```
 
@@ -54,15 +55,15 @@ A default configuration is loaded automatically and so the simplest method of pr
 `run_topostats` in the same directory as your scans _after_ having activated the virtual environment in which you have
 installed TopoStats
 
-``` bash
+```bash
 run_topostats
 ```
 
 If you have your own YAML configuration file (see [Usage : Configuring
 TopoStats](https://afm-spm.github.io/TopoStats/main/usage.html#configuring_topostats)) then invoke `run_topostats` and use
 the argument for `--config <config_file>.yaml` that points to your file.
 
-``` bash
+```bash
 # Edit and save my_config.yaml then run TopoStats with this configuration file
 run_topostats --config my_config.yaml
 ```
@@ -71,19 +72,19 @@ The configuration file is validated before analysis begins and if there are prob
 are hopefully useful in resolving the error(s) in your modified configuration.
 
 You can generate a sample configuration file using the `--create-config-file` argument which takes a single argument,
-the name of the file to save the configuration to (e.g. `config.yaml` or `settings.yaml`). This will _not_  run any
+the name of the file to save the configuration to (e.g. `config.yaml` or `settings.yaml`). This will _not_ run any
 analyses but will instead write the default configuration to the file `config.yaml` in the current directory.
 
 **NB** - This feature is only available in versions > v2.0.0 as it was introduced after v2.0.0 was released.
 
-``` bash
+```bash
 run_topostats --create-config-file config.yaml
 ```
 
 ### Notebooks
 
 Example Jupyter Notebooks are in have been developed that show how to use TopoStats package interactively which is
-useful when you are unsure of what parameters are most suited to your scans.  Other notebooks exist which show how to
+useful when you are unsure of what parameters are most suited to your scans. Other notebooks exist which show how to
 produce plots of the summary grain and tracing statistics or how to generate plots of scans from processed images which
 saves having to run the processing again. See the documentation on
 [Notebooks](https://afm-spm.github.io/TopoStats/main/notebooks.html) for further details.